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Holsinger2001 - The neutral theory of molecular evolution...

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The neutral theory of molecular evolution Introduction I didn’t make a big deal of it in what we just went over, but in deriving the Jukes-Cantor equation I used the phrase “substitution rate” instead of the phrase “mutation rate.” As a preface to what is about to follow, let me explain the difference. Mutation rate refers to the rate at which changes are incorporated into a nucleotide sequence during the process of reproduction, i.e., the probability that an allele in an organism differs from the copy of that in its parent from which it was derived. An allele substitution occurs when a newly arisen allele completely replaces other alleles in a population in which it arises, i.e., when a newly arisen allele becomes fixed in a population. Substitution rate refers to the rate at which allele substitutions occur. As we’ll see, mutation rates and substitution rates are related — substitutions can’t hap- pen unless mutations occur, after all — , but it’s important to remember that they refer to different processes. Early empirical observations By the early 1960s amino acid sequences of hemoglobins and cytochrome c for many mam- mals had been determined. When the sequences were compared, investigators began to notice that the number of amino acid differences between different pairs of mammals seemed to be roughly proportional to the time since they had diverged from one another, as inferred from the fossil record. Zuckerkandl and Pauling [8] proposed the molecular clock hypothesis to explain these results. Specifically, they proposed that there was a constant rate of amino acid substitution over time. Sarich and Wilson [6, 7] used the molecular clock hypothesis to propose that humans and apes diverged approximately 5 million years ago. While that proposal may not seem particularly controversial now, it generated enormous controversy at c circlecopyrt 2001-2006 Kent E. Holsinger
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the time, because at the time many paleoanthropologists interpreted the evidence to indicate humans diverged from apes as much as 30 million years ago. One year after Zuckerkandl and Pauling’s paper, Harris [1] and Hubby and Lewontin [2, 5] showed that protein electrophoresis could be used to reveal surprising amounts of genetic variability within populations. Harris studied 10 loci in human populations, found three of them to be polymorphic, and identified one locus with three alleles. Hubby and Lewontin studied 18 loci in Drosophila pseudoobscura , found seven to be polymorphic, and five that had three or more alleles. Both sets of observations posed real challenges for evolutionary geneticists. It was difficult to imagine an evolutionary mechanism that could produce a constant rate of substitution.
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